r2906 - in /branches/test_suite: generic_fns/ prompt/ sample_scripts/ -- December 02, 2006 - 05:53

Author: bugman
Date: Sat Dec  2 05:53:03 2006
New Revision: 2906

URL: http://svn.gna.org/viewcvs/relax?rev=2906&view=rev
Log:
Ported r2850 to r2852 from the 1.3 line.

The command used was:
svn merge -r2849:2852 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3


Added:
    branches/test_suite/prompt/reset.py
      - copied unchanged from r2852, 1.3/prompt/reset.py
Removed:
    branches/test_suite/prompt/init_data.py
Modified:
    branches/test_suite/generic_fns/__init__.py
    branches/test_suite/prompt/__init__.py
    branches/test_suite/prompt/interpreter.py
    branches/test_suite/sample_scripts/angles.py
    branches/test_suite/sample_scripts/dasha.py
    branches/test_suite/sample_scripts/diff_min.py
    branches/test_suite/sample_scripts/full_analysis.py
    branches/test_suite/sample_scripts/mf_multimodel.py
    branches/test_suite/sample_scripts/model-free.py
    branches/test_suite/sample_scripts/noe.py
    branches/test_suite/sample_scripts/palmer.py
    branches/test_suite/sample_scripts/relax_fit.py

Modified: branches/test_suite/generic_fns/__init__.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/generic_fns/__init__.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/generic_fns/__init__.py (original)
+++ branches/test_suite/generic_fns/__init__.py Sat Dec  2 05:53:03 2006
@@ -35,11 +35,11 @@
             'monte_carlo',
             'nuclei',
             'palmer',
-            'pdb',
             'results',
             'runs',
             'selection',
             'sequence',
             'state',
+            'structure',
             'value',
             'vmd' ]

Modified: branches/test_suite/prompt/__init__.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/prompt/__init__.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/prompt/__init__.py (original)
+++ branches/test_suite/prompt/__init__.py Sat Dec  2 05:53:03 2006
@@ -31,7 +31,6 @@
            'gpl',
            'grace',
            'help',
-           'init_data'
            'interpreter',
            'jw_mapping',
            'minimisation',
@@ -42,15 +41,16 @@
            'noe',
            'nuclei',
            'palmer',
-           'pdb',
            'pymol',
            'relax_data',
            'relax_fit',
+           'reset',
            'run',
            'rw',
            'select',
            'sequence',
            'state',
+           'structure',
            'thread',
            'tab_completion',
            'unselect',

Modified: branches/test_suite/prompt/interpreter.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/prompt/interpreter.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/prompt/interpreter.py (original)
+++ branches/test_suite/prompt/interpreter.py Sat Dec  2 05:53:03 2006
@@ -43,7 +43,7 @@
 from eliminate import Eliminate
 from fix import Fix
 from gpl import GPL
-from init_data import Init_data
+from reset import Reset
 from minimisation import Minimisation
 from model_selection import Modsel
 from nuclei import Nuclei
@@ -98,7 +98,7 @@
         self._Eliminate = Eliminate(relax)
         self._Fix = Fix(relax)
         self._GPL = GPL
-        self._Init_data = Init_data(relax)
+        self._Reset = Reset(relax)
         self._Minimisation = Minimisation(relax)
         self._Modsel = Modsel(relax)
         self._Nuclei = Nuclei(relax)
@@ -158,7 +158,7 @@
         eliminate = self._Eliminate.eliminate
         fix = self._Fix.fix
         grid_search = self._Minimisation.grid_search
-        init_data = self._Init_data.init
+        reset = self._Reset.reset
         minimise = self._Minimisation.minimise
         model_selection = self._Modsel.model_selection
         nuclei = self._Nuclei.nuclei

Modified: branches/test_suite/sample_scripts/angles.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/sample_scripts/angles.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/sample_scripts/angles.py (original)
+++ branches/test_suite/sample_scripts/angles.py Sat Dec  2 05:53:03 2006
@@ -1,5 +1,5 @@
 name = 'spheroid'
 run.create(name, 'mf')
-pdb(name, "Ap4Aase_new_3.pdb")
+structure.read_pdb(name, "Ap4Aase_new_3.pdb")
 diffusion_tensor.init(name, (1.698e7, 1.417e7, 67.174, -83.718), 
param_types=3)
 angles(name)

Modified: branches/test_suite/sample_scripts/dasha.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/sample_scripts/dasha.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/sample_scripts/dasha.py (original)
+++ branches/test_suite/sample_scripts/dasha.py Sat Dec  2 05:53:03 2006
@@ -16,7 +16,7 @@
     sequence.read(name, 'noe.500.out')
 
     # Load a PDB file.
-    #pdb(name, 'example.pdb')
+    #structure.read_pdb(name, 'example.pdb')
 
     # Load the relaxation data.
     relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')

Modified: branches/test_suite/sample_scripts/diff_min.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/sample_scripts/diff_min.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/sample_scripts/diff_min.py (original)
+++ branches/test_suite/sample_scripts/diff_min.py Sat Dec  2 05:53:03 2006
@@ -22,7 +22,7 @@
     sequence.read(name, 'noe.500.out')
 
     # Load a PDB file.
-    pdb(name, 'example.pdb')
+    structure.read_pdb(name, 'example.pdb')
 
     # Load the relaxation data.
     relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')

Modified: branches/test_suite/sample_scripts/full_analysis.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/sample_scripts/full_analysis.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/sample_scripts/full_analysis.py (original)
+++ branches/test_suite/sample_scripts/full_analysis.py Sat Dec  2 05:53:03 
2006
@@ -171,7 +171,7 @@
                 model_free.remove_tm(run=name)
 
                 # Load the PDB file.
-                pdb(name, '1F3Y.pdb')
+                structure.read_pdb(name, '1F3Y.pdb')
 
                 # Add an arbitrary diffusion tensor which will be optimised.
                 if self.diff_model == 'sphere':
@@ -377,7 +377,7 @@
 
             # Load the PDB file.
             if not local_tm:
-                pdb(name, '1F3Y.pdb')
+                structure.read_pdb(name, '1F3Y.pdb')
 
             # Load the relaxation data.
             relax_data.read(name, 'R1', '600', 599.719 * 1e6, 'r1.600.out')

Modified: branches/test_suite/sample_scripts/mf_multimodel.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/sample_scripts/mf_multimodel.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/sample_scripts/mf_multimodel.py (original)
+++ branches/test_suite/sample_scripts/mf_multimodel.py Sat Dec  2 05:53:03 
2006
@@ -16,7 +16,7 @@
     sequence.read(name, 'noe.500.out')
 
     # Load a PDB file.
-    #pdb(name, 'example.pdb')
+    #structure.read_pdb(name, 'example.pdb')
 
     # Load the relaxation data.
     relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')

Modified: branches/test_suite/sample_scripts/model-free.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/sample_scripts/model-free.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/sample_scripts/model-free.py (original)
+++ branches/test_suite/sample_scripts/model-free.py Sat Dec  2 05:53:03 2006
@@ -11,7 +11,7 @@
 sequence.read(name, 'noe.500.out')
 
 # Load a PDB file.
-#pdb(name, 'example.pdb')
+#structure.read_pdb(name, 'example.pdb')
 
 # Load the relaxation data.
 relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')

Modified: branches/test_suite/sample_scripts/noe.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/sample_scripts/noe.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/sample_scripts/noe.py (original)
+++ branches/test_suite/sample_scripts/noe.py Sat Dec  2 05:53:03 2006
@@ -5,7 +5,7 @@
 run.create(name, 'noe')
 
 # Load the sequence from a PDB file.
-pdb(name, 'Ap4Aase_new_3.pdb', load_seq=1)
+structure.read_pdb(name, 'Ap4Aase_new_3.pdb', load_seq=1)
 
 # Load the reference spectrum and saturated spectrum peak intensities.
 noe.read(name, file='ref.list', spectrum_type='ref')

Modified: branches/test_suite/sample_scripts/palmer.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/sample_scripts/palmer.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/sample_scripts/palmer.py (original)
+++ branches/test_suite/sample_scripts/palmer.py Sat Dec  2 05:53:03 2006
@@ -27,7 +27,7 @@
         sequence.read(name, 'noe.500.out')
 
         # PDB.
-        #pdb(name, 'Ap4Aase_new_3.pdb')
+        #structure.read_pdb(name, 'Ap4Aase_new_3.pdb')
 
         # Load the relaxation data.
         relax_data.read(name, 'R1', '600', 600.0 * 1e6, 'r1.600.out')

Modified: branches/test_suite/sample_scripts/relax_fit.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/test_suite/sample_scripts/relax_fit.py?rev=2906&r1=2905&r2=2906&view=diff
==============================================================================
--- branches/test_suite/sample_scripts/relax_fit.py (original)
+++ branches/test_suite/sample_scripts/relax_fit.py Sat Dec  2 05:53:03 2006
@@ -5,7 +5,7 @@
 run.create(name, 'relax_fit')
 
 # Load the sequence from a PDB file.
-pdb(name, 'Ap4Aase_new_3.pdb', load_seq=1)
+structure.read_pdb(name, 'Ap4Aase_new_3.pdb', load_seq=1)
 
 # Load the peak intensities.
 relax_fit.read(name, file='T2_ncyc1.list', relax_time=0.0176)